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NIAS-Server 2.0: A versatile complementary tool for structural biology studies.

Bruno César Feltes1, Éderson Sales Moreira Pinto2, Arthur Tonietto Mangini2

  • 1Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.

Journal of Computational Chemistry
|April 11, 2023
PubMed
Summary

The updated Neighbors Influence of Amino Acids and Secondary Structures (NIAS) server provides enhanced protein structure analysis. It now includes diverse data types and years, improving conformational preference insights for structural biology.

Keywords:
angle-probability listbioinformaticsmutationprotein structuresecondary structurestructural biology

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Advancing protein structure knowledge requires diverse analytical tools.
  • The Neighbors Influence of Amino Acids and Secondary Structures (NIAS) server analyzes amino acid conformational preferences.
  • NIAS utilizes the Angle Probability List based on empirical conformational preferences from the Protein Data Bank.

Purpose of the Study:

  • To announce the updated NIAS server with expanded data.
  • To incorporate a wider range of structural data beyond X-ray crystallography.
  • To demonstrate NIAS as a complementary tool in structural biology research.

Main Methods:

  • Updated NIAS server with data up to September 2022.
  • Integrated data from solid-state NMR, solution NMR, CullPDB, Electron Microscopy, and Electron Crystallography.
  • Applied multiple filtering parameters to the expanded dataset.

Main Results:

  • The NIAS server now includes 7 years of additional structural data.
  • The inclusion of diverse structural data sources broadens the analysis scope.
  • Examples illustrate NIAS's application in various structural biology contexts.

Conclusions:

  • The updated NIAS server offers a more comprehensive resource for analyzing protein conformational preferences.
  • Expanded data and methods enhance NIAS's utility as a complementary tool.
  • Understanding NIAS's applications and limitations is crucial for its effective use.